Around ten years later, Soong was captured by Earth forces and imprisoned for his crimes, leaving his "children" to finish their own raising. While he was gone, Raakin came to become the leader of the little band of Augments.

In May 2154, two of the Augments, Malik and Saul, managed to make it off-planet in a transport pod. They were picked up by a Klingon Bird-of-Prey in the Borderland. The Augments managed to fight off the Klingon crew, and ejected their bodies into space. They then took the Bird-of-Prey back to Trialas to pick up the other Augments. Raakin took charge of the Bird-of-Prey, but was killed by Malik in a power struggle, thanks to some assistance from Persis.

The Klingons recovered the bodies of their dead crew from space, and DNA traces left on the bodies revealed they had been killed by Humans. Klingon chancellorM'Rek threatened to retaliate with extreme force, but the EarthStarfleet realized the DNA on the bodies matched that of Soong's Augments.

Starfleet assigned the recently-refit Enterprise NX-01 to capture the rogue Augments in order to stop the threatened war with the Klingons. CaptainJonathan Archer called upon the help of a reluctant Arik Soong to help to capture the Augments.

Upon crossing into the Borderland on May 17, Enterprise encountered two Orion interceptors, which kidnapped nine members of Enterprise's crew (including CommanderT'Pol and EnsignJeffrey Pierce). With help of Soong, Enterprise was able to find the kidnapped crew on Verex III, an Orion processing planet for slaves. During the rescue, Soong nearly escaped. Though he was prevented, he did manage to transmit a signal to the Augments.

Enterprise departed Verex, but the Orions caught up with the ship and attacked it again, causing damage to the engines. The Augments arrived in the Bird-of-Prey, responding to Soong's signal, and assisted in deterring the Orions. During a conversation with Malik in his ready room, Archer was taken hostage and used to retrieve Soong from Enterprise's brig. Archer was released and the Bird-of-Prey escaped with Soong.

Soong's goal was to revive the thousands of other Augment embryos at Cold Station 12, and so the Bird-of-Prey headed there. The DenobulanshuttleBarzai was captured by the Augments and its pilot imprisoned. The Barzai was used to gain access to Cold Station 12. When inside, the Augments had no problem incapacitating the guards. Accessing the stations environmental systems, all the scientists on board were knocked out as the Augments took over the main command center. The scientists were imprisoned in the command center by the Augments.

The station's lead scientist Doctor Jeremy Lucas was questioned by Soong as to the authorization code to access the embryos. When Lucas was unresponsive, one of the scientists was placed in a chamber where Symbalene blood burn was released. Despite his colleague being in a large amount of pain and dying, Lucas did not reveal the codes. After some time, Soong released the antipathogen in the chamber, but it was too late: the scientist had died.

Meanwhile, Enterprise was trying to discover where Soong had gone. Bereft of clues, the ship journeyed to Trialas IV, where they encountered an Augment, abandoned by his "siblings", named Udar ("Smike"). They also noted that incubators and artificial wombs had been removed from the planet, indicating Soong's intentions to recover more embryos. Armed with this information, Enterprise headed for C-12.

When the ship approached the asteroid belt where C-12 was located, the Augments located the ship and threatened to kill Lucas if Enterprise did not leave the field. Archer complied and Enterprise proceeded to leave the field. With another plan in mind, a boarding party was prepared (consisting of Archer and Phlox, among others); the party would beam aboard C-12 right before Enterprise went out of range. The team was beamed over but still detected not long after their arrival when Phlox disconnected the life support relays to the command center.

The Enterprise team was sent into the command center, but this time Soong put Doctor Phlox into a chamber to get Lucas to talk, as the two were old friends. This time, Soong was successful and Lucas gave the command codes, for which Soong released Phlox. Enterprise was hailed by Soong and told them that the boarding party had been captured. Archer managed to order T'Pol to activate the station's auto-destruct over the commline.

The auto-destruct failed due to a lockout by the Augments, and when the Enterprise was attacked by the Bird-of-Prey, Enterprise's engines were damaged again. Soong and Malik proceeded to the embryo chamber and prepared all of them for transport. Malik lowered all the containment fields for the pathogens on C-12; Udar was killed in his confrontation with Archer. The Augments subsequently escaped the system in their Bird-of-Prey.

Archer managed to stop the pathogens from infecting the command center, though the rest of the station would need massive amounts of decontamination. He ended up with a mild case of decompression in the effort.

Soong wanted to end the confrontation with Enterprise by raising the embryos on a planet in Klach D'kel Brakt, in Klingon territory. Malik, however, wished to confront Enterprise again; the "father" and "son" also clashed when Malik learned Soong was trying to make the new Augments less violent.

Enterprise caught up to the Bird-of-Prey and attacked it, almost crippling the vessel, but Soong devised a plan and put the pilot of the Barzai back into her shuttle and dropped it into the atmosphere of a planet. With Enterprise consumed with a rescue mission, the Bird-of-Prey was able to escape.

Malik talked with Soong afterward, telling him he had created a biogenic weapon using pathogens from C-12. He planned to drop it on the Klingon Qu'Vat colony and spark a war between Humans and Klingons to distract them from the Augments. Soong greatly disapproved of this idea, which enraged Malik even more, prompting a mutiny. Soong was confined to quarters while Malik took command. Persis helped Soong to escape the Bird-of-Prey in an escape pod in hopes of finding Enterprise. Malik later killed Persis when he learned what she had done.

Commander Tucker altered Enterprise's warp signature to Klingon specifications to chase the Augments through Klingon space; however the ship inadvertently passed into a restricted star system governed by Klag. With the Klingons demanding to inspect the ship, Archer bluffed them into believing they were transporting the chancellor from talks with the Orion Syndicate.

D5 grappled by Enterprise

Shortly after that, Enterprise found the pod with Soong on board. Soong revealed Malik's plan, giving even Enterprise further impetus to catch the Augments. The Enterprise encountered a Klingon D5 class battle cruiser, which knew they were Starfleet. A battle ensued, but Enterprise dropped out of warp and used its grappling hooks to damage a nacelle on the D5. With the other vessel incapacitated, Enterprise continued on, with Soong's guidance.

The bird-of-prey arrived at the Qu'Vat colony with Enterprise only about a minute behind. The biogenic torpedo was prepared and fired, just as Enterprise arrived at the planet. Malcolm Reed targeted the torpedo and launched a few photonic torpedoes; fortunately the Starfleet torpedoes were swifter, and the biogenic weapon was harmlessly detonated above the atmosphere.

The Augments then retaliated against Enterprise, causing major damage to the armory. At Soong instruction, Enterprise targeted a section of the Bird-of-Prey that lacked dispersive armor with their only phase cannon and caused major damage to the bird-of-prey.

The Bird of Prey is destroyed

Malik, despite entreaties by Soong, overloaded the dilithium matrix and destroyed the Bird-of-Prey, killing the last of the Augments. Malik somehow made his way aboard Enterprise in a last attempt to kill Soong, but he was shot by Archer and finally died.

Satisfied by the actions of Enterprise at Qu'Vat, on May 27 the Klingon High Council agreed to not retaliate against Earth.

Enterprise returned to Earth for repairs, and Soong was sent back to prison. Soong told Archer that he thought perfecting Humanity through genetics was not possible, and that the answer might lie in cybernetics. Interestingly, in the 24th century, Doctor Noonian Soong (a descendant of Arik) created several functioning androids.

When the Klingons investigated the battle at Qu'Vat colony, a number of embryos were retrieved. The DNA of these embryos were used by the Klingons in tests to make Klingon Augments. Unfortunately, this resulted in the outbreak of a dangerous virus that threatened the entire species.